NM_020949.3:c.-152-6678T>C

Variant names:

• chr3-170533766-A-G
• rs10513682
• NM_020949.3:c.-152-6678T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020949.3(SLC7A14):​c.-152-6678T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,048 control chromosomes in the GnomAD database, including 1,440 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (1440 hom., cov: 33)
• Consequence: SLC7A14 NM_020949.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.354
• Publications: 6 publications found

Genes affected

SLC7A14 (HGNC:29326): (solute carrier family 7 member 14) This gene is predicted to encode a glycosylated, cationic amino acid transporter protein with 14 transmembrane domains. This gene is primarily expressed in skin fibroblasts, neural tissue, and primary endothelial cells and its protein is predicted to mediate lysosomal uptake of cationic amino acids. Mutations in this gene are associated with autosomal recessive retinitis pigmentosa. In mice, this gene is expressed in the photoreceptor layer of the retina where its expression increases over the course of retinal development and persists in the mature retina. [provided by RefSeq, Apr 2014]

ENSG00000285218 (HGNC:):

SLC7A14-AS1 (HGNC:54092): (SLC7A14 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC7A14	NM_020949.3	c.-152-6678T>C		intron_variant	Intron 1 of 7	ENST00000231706.6	NP_066000.2
SLC7A14-AS1	NR_135555.1	n.215+56893A>G		intron_variant	Intron 2 of 2
SLC7A14-AS1	NR_135556.1	n.215+56893A>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC7A14	ENST00000231706.6	c.-152-6678T>C		intron_variant	Intron 1 of 7	2	NM_020949.3	ENSP00000231706.4
ENSG00000285218	ENST00000486975.1	c.391+110439A>G		intron_variant	Intron 2 of 3	2		ENSP00000417434.1

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20769 AN: 151930 Hom.: 1439 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.0723

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.143

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.137 AC: 20784 AN: 152048 Hom.: 1440 Cov.: 33 AF XY: 0.137 AC XY: 10179 AN XY: 74320

African (AFR) AF: 0.108 AC: 4467 AN: 41482

American (AMR) AF: 0.179 AC: 2738 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0723 AC: 251 AN: 3470

East Asian (EAS) AF: 0.172 AC: 885 AN: 5144

South Asian (SAS) AF: 0.145 AC: 699 AN: 4820

European-Finnish (FIN) AF: 0.132 AC: 1396 AN: 10556

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9893 AN: 67978

Other (OTH) AF: 0.141 AC: 299 AN: 2114

Alfa AF: 0.138 Hom.: 2091

Bravo AF: 0.138

Asia WGS AF: 0.173 AC: 599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.54
PhyloP100		0.35
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10513682; hg19: chr3-170251555;